Define conformer single point calculation after optimization #766

JintaoWu98 · 2024-09-15T01:44:55Z

We change the name of job_type conformers to conf_opt.
We define a new job_type conf_sp.
We can now calculate the sp value after the optimization job using the level of theory in conformer_sp_level.
Save the conformers_after_optimization.txt using the updated level of theory and energies specified in conformer_sp_level, if it is being used.

codecov · 2024-09-15T03:22:06Z

Codecov Report

Attention: Patch coverage is 40.00000% with 69 lines in your changes missing coverage. Please review.

Project coverage is 74.04%. Comparing base (fb16f4a) to head (9444375).
Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
arc/scheduler.py	7.69%	42 Missing and 6 partials ⚠️
arc/main.py	46.66%	5 Missing and 3 partials ⚠️
arc/checks/common.py	33.33%	1 Missing and 1 partial ⚠️
arc/job/adapters/orca.py	0.00%	0 Missing and 2 partials ⚠️
arc/job/adapters/qchem.py	0.00%	1 Missing and 1 partial ⚠️
arc/job/adapters/terachem.py	0.00%	2 Missing ⚠️
arc/job/trsh.py	0.00%	0 Missing and 2 partials ⚠️
arc/plotter.py	33.33%	1 Missing and 1 partial ⚠️
arc/job/adapters/cfour.py	50.00%	0 Missing and 1 partial ⚠️

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@@            Coverage Diff             @@
##             main     #766      +/-   ##
==========================================
- Coverage   74.09%   74.04%   -0.06%     
==========================================
  Files         101      101              
  Lines       28005    28030      +25     
  Branches     5860     5870      +10     
==========================================
+ Hits        20751    20754       +3     
- Misses       5786     5802      +16     
- Partials     1468     1474       +6

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alongd

Looking good! I added some minor comments and questions

alongd · 2024-10-18T08:32:25Z

arc/main.py

@@ -169,6 +170,7 @@ class ARC(object):
        level_of_theory (str): A shortcut representing either sp//geometry levels or a composite method.
        composite_method (Level): Composite method.
        conformer_opt_level (Level): Level of theory for conformer searches.
+        conformer_sp_level (str, dict, Level, optional): Level of theory for conformer sp jobs after opt.


please remove "optional" (arguments can be optional, not attributes)
Why are the types of conformer_opt_level and conformer_sp_level different?

The difference was a mistake, it's fixed now.

alongd · 2024-10-18T08:46:56Z

arc/settings/settings.py

@@ -91,6 +91,7 @@

 # List here job types to execute by default
 default_job_types = {'conf_opt': True,      # defaults to True if not specified
+                     'conf_sp': False,      # defaults to True if not specified


please fix the comment to False as well (also align)

alongd · 2024-10-18T08:51:35Z

arc/plotter.py

+            if not sp_flag:
+                content += f'Conformers for {label}, optimized at the {level_of_theory} level:\n\n'
+            else:
+                content += f'Conformers for {label}, single point calculation at the {level_of_theory} level:\n\n'


will ARC now save two files, for conf_opt and for conf_sp, or will it override one?

In our previous discussion, we wanted to overwrite it, meaning conf_sp will overwrite conf_opt if it exists. But feel free to let me know if we need to change it.

alongd · 2024-10-18T09:11:11Z

arc/scheduler.py

@@ -547,20 +547,27 @@ def schedule_jobs(self):
                    continue
                job_list = self.running_jobs[label]
                for job_name in job_list:
-                    if 'conformer' in job_name:
+                    if 'conf_opt' in job_name or 'conf_sp' in job_name:


maybe check here if 'conf_' in job_name?

alongd · 2024-10-18T09:12:15Z

arc/scheduler.py

+                                                 xyz=self.species_dict[label].conformers[i],
+                                                 level_of_theory=self.conformer_sp_level,
+                                                 job_type='conf_sp',
+                                                 conformer=i,)


you can remove the comma at the end here

alongd · 2024-10-18T09:16:43Z

arc/scheduler.py

+                self.job_dict[label]['conf_opt'] = dict()
+            if 'conf_sp' not in self.job_dict[label] and job_type == 'conf_sp':
+                self.job_dict[label]['conf_sp'] = dict()
+            if job_type == 'conf_opt':


Do you think we can replace these four lines with
self.job_dict[label][job_type][conformer] = job # save job object
?

arc/scheduler.py

alongd · 2024-10-18T09:22:15Z

arc/scheduler.py

                                content += job_name + ', '
-                            elif job_type == 'conformers':
+                            elif job_type == 'conf_opt':


shall we also restore conf_sp jobs here?

arc/testing/restart/1_restart_thermo/restart.yml

At this branch, we would like to define a new job_type during our conformer search, `conf_sp`, which will be run after the conformer optimization job. Thus, we want to distinguish them by giving a new name `conf_opt`.

alongd

Thanks!

This is a follow-up to PR #766 and aims to refine the existing implementation by adhering to a consistent job naming standard.

Change conformer_level to conformer_opt_level

0e64c33

github-actions bot added Module: Main Module: Plotter Module: Scheduler labels Sep 15, 2024

JintaoWu98 force-pushed the conf_opt_level branch 2 times, most recently from 47882b1 to 0577e94 Compare September 16, 2024 11:08

JintaoWu98 force-pushed the conf_opt_level branch 2 times, most recently from 0107934 to 0577e94 Compare September 26, 2024 04:17

JintaoWu98 force-pushed the conf_opt_level branch from 0577e94 to 17e1b1a Compare October 7, 2024 08:18

JintaoWu98 force-pushed the conf_opt_level branch from 17e1b1a to 9378423 Compare October 17, 2024 09:10

github-actions bot added Module Functional Module: trsh Troubleshooting labels Oct 17, 2024

JintaoWu98 changed the title ~~Define conformer_sp_level~~ Define conformer single point calculation after optimization Oct 17, 2024

JintaoWu98 requested a review from alongd October 17, 2024 13:35

alongd reviewed Oct 18, 2024

View reviewed changes

JintaoWu98 added 4 commits October 18, 2024 17:59

Define conformer_sp_level

c19e9b3

Change job_type 'conformers' to 'conf_opt'

f32d7c1

At this branch, we would like to define a new job_type during our conformer search, `conf_sp`, which will be run after the conformer optimization job. Thus, we want to distinguish them by giving a new name `conf_opt`.

Define new job_type conf_sp

4ccd091

Consider conf_sp job_type in the output folder txt files

b0e483f

JintaoWu98 force-pushed the conf_opt_level branch from 9378423 to 955311e Compare October 18, 2024 10:24

JintaoWu98 force-pushed the conf_opt_level branch from 281fa05 to 74e8d50 Compare November 2, 2024 12:17

JintaoWu98 added 3 commits November 3, 2024 19:33

Run conf_sp job after conf_opt job is finished

53c1e3c

Consistency for conf_opt and conf_sp in scheduler files

a7a15d4

Consistency in restart and source files

9444375

JintaoWu98 force-pushed the conf_opt_level branch from 74e8d50 to 9444375 Compare November 3, 2024 11:34

alongd approved these changes Nov 4, 2024

View reviewed changes

alongd merged commit f20c453 into main Nov 4, 2024
5 of 7 checks passed

alongd deleted the conf_opt_level branch November 4, 2024 06:20

JintaoWu98 mentioned this pull request Dec 1, 2024

patch/pr-711-name-format #776

Merged

calvinp0 added a commit that referenced this pull request Dec 2, 2024

patch/pr-711-name-format (#776)

84898ee

This is a follow-up to PR #766 and aims to refine the existing implementation by adhering to a consistent job naming standard.

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Define conformer single point calculation after optimization #766

Define conformer single point calculation after optimization #766

JintaoWu98 commented Sep 15, 2024 •

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Define conformer single point calculation after optimization #766

Define conformer single point calculation after optimization #766

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JintaoWu98 commented Sep 15, 2024 •

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